Variant report

Variant	rs3002700
Chromosome Location	chr20:25292962-25292963
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr20:25292825-25293071	GM12878	blood:	n/a	n/a
2	PAX5	chr20:25292827-25293091	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25290481..25292963-chr20:25369877..25371974,2	MCF-7	breast:

Variant related genes	Relation type
ABHD12	TF binding region
ENSG00000100997	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs2039400	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2258671	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2258672	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474768	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474770	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474772	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2474776	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482907	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482909	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482916	1.00[AMR][1000 genomes]
rs2482917	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482922	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482925	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482929	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482939	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482942	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482945	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500394	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500396	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500402	1.00[AMR][1000 genomes]
rs2500407	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500409	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500411	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500412	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500414	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500416	1.00[ASN][1000 genomes]
rs2500419	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500420	1.00[AMR][1000 genomes]
rs2500428	1.00[ASN][1000 genomes]
rs2500429	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500431	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500434	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500435	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2500437	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500438	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500440	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500444	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500445	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500447	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2983490	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2990514	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2990515	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002703	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs364722	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs366060	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs368636	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs368748	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs378534	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs379538	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs380021	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs384336	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs400916	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs423248	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs426143	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs428801	1.00[ASN][1000 genomes]
rs429120	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs432403	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs448866	1.00[AMR][1000 genomes]
rs518336	1.00[AMR][1000 genomes]
rs56165312	1.00[ASN][1000 genomes]
rs6037089	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037112	1.00[ASN][1000 genomes]
rs6037113	1.00[ASN][1000 genomes]
rs6037119	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60483717	1.00[ASN][1000 genomes]
rs6050480	0.81[AFR][1000 genomes]
rs6050591	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050613	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050618	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050627	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050628	1.00[ASN][1000 genomes]
rs73904034	0.81[AFR][1000 genomes]
rs73904036	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904038	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904039	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904476	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73907308	1.00[ASN][1000 genomes]
rs73907312	1.00[ASN][1000 genomes]
rs73907315	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	esv1798601	chr20:25250122-25305949	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25256000-25299400	Weak transcription	Fetal Brain Male	brain
2	chr20:25278800-25305600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr20:25284600-25304000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr20:25288400-25294400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr20:25289200-25304600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr20:25289400-25302400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr20:25289600-25293000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr20:25289800-25299400	Weak transcription	Brain Germinal Matrix	brain
9	chr20:25290000-25294400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr20:25290200-25293000	Enhancers	Spleen	Spleen
11	chr20:25290200-25297000	Weak transcription	Fetal Brain Female	brain
12	chr20:25290800-25300200	Weak transcription	Fetal Lung	lung
13	chr20:25291400-25294400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr20:25291600-25293000	Enhancers	Small Intestine	intestine
15	chr20:25291600-25294400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr20:25291600-25298200	Weak transcription	Primary B cells from cord blood	blood
17	chr20:25291800-25293000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr20:25291800-25294800	Weak transcription	Pancreas	Pancrea
19	chr20:25291800-25295200	Weak transcription	Fetal Kidney	kidney
20	chr20:25291800-25297600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr20:25292000-25293000	Enhancers	Brain Hippocampus Middle	brain
22	chr20:25292000-25294400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr20:25292000-25295400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr20:25292000-25297200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr20:25292000-25298400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr20:25292000-25299600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr20:25292000-25310000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr20:25292000-25325200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr20:25292000-25327400	Weak transcription	Aorta	Aorta
30	chr20:25292200-25293000	Enhancers	Fetal Heart	heart
31	chr20:25292200-25293000	Enhancers	A549	lung
32	chr20:25292200-25293200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
33	chr20:25292200-25293400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr20:25292200-25294200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr20:25292200-25294400	Weak transcription	Dnd41	blood
36	chr20:25292200-25294800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr20:25292200-25295000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr20:25292200-25295000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr20:25292200-25295200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr20:25292200-25295400	Weak transcription	Primary T cells from cord blood	blood
41	chr20:25292200-25295600	Weak transcription	Right Ventricle	heart
42	chr20:25292200-25295800	Weak transcription	HMEC	breast
43	chr20:25292200-25296000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr20:25292200-25296000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr20:25292200-25297000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr20:25292200-25297600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr20:25292200-25298000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr20:25292200-25299600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr20:25292200-25303600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr20:25292200-25303800	Weak transcription	HUVEC	blood vessel

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